[BioC] arrayQualityMetrics error and question
Wolfgang Huber
whuber at embl.de
Tue Mar 6 22:31:05 CET 2012
Dear David
Mar/5/12 11:04 PM, David Westergaard scripsit::
> Hi,
>
> It seems to be working now, with arrayQualityMetrics v3.10. The only
> "problem" is, I am getting alot of warnings, more than 50.
> All of them are:
> In grid.Call.graphics(L_segments, x$x0, x$y0, x$x1, x$y1, ... :
> X11 protocol error: BadMatch (invalid parameter attributes)
>
> Can I just disregard these? Reports are still being produced.
I have never seen these before. It might be a problem specific to your
(slightly broken?) R installation.
> Also, have methods changed from arrayQualityMetrics 2.6.0 -> 3.10?
> Some arrays which previously did not pass some tests, not pass the
> tests. And vice versa.
Yes. Hence the different major version number. The new methods for
outlier detection are documented in the report - please let me know if
you have questions or comments about these.
Of course, outlier detection is a poorly defined question, and there is
no 'right' or 'wrong' answer. These are hints which are intended to be
followed up manually. If you want to automate outlier detection, you
need to limit the scope to a particular platform and experimental
design, and then choose and calibrate the metrics used. I have added an
extra note to this effect to the introduction of the report.
Best wishes
Wolfgang
> For instance, in version 2.6.0, using data from
> http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-2261, 2 arrays
> failed 1 test (p0742_O11_120_24.CEL and p0742_O3_000_11.CEL), 1 array
> failed 2 tests (p0742_O3_120_12.CEL), and 1 array failed 3 tests
> (p0742_O15_120_40.CEL
> In version 3.10, 1 array failed 1 test (p0742_O3_120_12.CEL) and 1
> array failed 2 tests (p0742_O15_120_40.CEL).
>
> Sessioninfo:
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: ia64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] nugohs1a520180cdf_2.4.1 hgu133plus2cdf_2.9.1
> [3] AnnotationDbi_1.16.18 affy_1.32.1
> [5] Biobase_2.14.0 arrayQualityMetrics_3.10.0
>
> loaded via a namespace (and not attached):
> [1] BiocInstaller_1.2.1 Biostrings_2.22.0 Cairo_1.5-1
> [4] DBI_0.2-5 Hmisc_3.9-2 IRanges_1.12.6
> [7] KernSmooth_2.23-7 RColorBrewer_1.0-5 RSQLite_0.11.1
> [10] SVGAnnotation_0.93-1 XML_3.9-4 affyPLM_1.30.0
> [13] affyio_1.22.0 annotate_1.32.1 beadarray_2.4.1
> [16] cluster_1.14.2 genefilter_1.36.0 grid_2.14.1
> [19] hwriter_1.3 lattice_0.20-0 latticeExtra_0.6-19
> [22] limma_3.10.3 preprocessCore_1.16.0 setRNG_2009.11-1
> [25] splines_2.14.1 survival_2.36-12 tools_2.14.1
> [28] vsn_3.22.0 xtable_1.7-0 zlibbioc_1.0.1
>
> Best,
> David
>
> 2012/3/5 David Westergaard<david at harsk.dk>:
>> Hi,
>>
>> I did not express myself clearly enough - I actually didn't have
>> trouble with beadarray. The package giving me trouble was Cairo, but I
>> solved that by installing newest cairoDevice pacakge, followed by
>> Cairo-1.4-5. I'm now running R-2.14 with arrayQualityMetrics v3.10 -
>> I'll let you know if I encounter any problems.
>>
>> Best,
>> David
>>
>> 2012/3/4 Dan Tenenbaum<dtenenba at fhcrc.org>:
>>> Hi,
>>>
>>> On Sun, Mar 4, 2012 at 2:44 PM, David Westergaard<david at harsk.dk> wrote:
>>>> Hi Wolfgang,
>>>>
>>>> The problem hasn't really resolved itself. I can't update any further,
>>>> since I'm having trouble installing arrayQualityMatrics with R-2.14 on
>>>> the server I have access to. (beadarray, which is a requirement, needs
>>>> R>=2.13)
>>>
>>> R 2.14 is>= R 2.13, so beadarray works on R-2.14.
>>> What is the specific error message (and sessionInfo()) you get when
>>> trying to install arrayQualityMetrics (or beadarray) on R 2.14?
>>>
>>> Dan
>>>
>>>
>>>> Cairo fails to install, giving two errors:
>>>> cairotalk.c:894: error: 'CAIRO_EXTEND_PAD' undeclared (first use in
>>>> this function)
>>>> cairotalk.c:322: error: 'CAIRO_SURFACE_TYPE_IMAGE' undeclared (first
>>>> use in this function)
>>>>
>>>> I can install both fine on my own computer, however, but I do not have
>>>> enough memory to process the files myself. Are there any options
>>>> besides spatial=FALSE to reduce memory usage?
>>>>
>>>>
>>>> Here's the output of sessionInfo()
>>>>> sessionInfo()
>>>> R version 2.11.0 (2010-04-22)
>>>> ia64-unknown-linux-gnu
>>>>
>>>> locale:
>>>> [1] C
>>>>
>>>> attached base packages:
>>>> [1] stats graphics grDevices utils datasets methods base
>>>>
>>>> other attached packages:
>>>> [1] arrayQualityMetrics_2.6.0 affyPLM_1.24.1
>>>> [3] preprocessCore_1.10.0 gcrma_2.20.0
>>>> [5] affy_1.26.1 Biobase_2.8.0
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] AnnotationDbi_1.10.0 Biostrings_2.16.9 DBI_0.2-5
>>>> [4] IRanges_1.6.8 RColorBrewer_1.0-2 RSQLite_0.9-4
>>>> [7] affyio_1.16.0 annotate_1.26.0 beadarray_1.16.0
>>>> [10] genefilter_1.30.0 grid_2.11.0 hwriter_1.2
>>>> [13] lattice_0.18-5 latticeExtra_0.6-18 limma_3.4.5
>>>> [16] marray_1.26.0 simpleaffy_2.24.0 splines_2.11.0
>>>> [19] stats4_2.11.0 survival_2.35-8 tools_2.11.0
>>>> [22] vsn_3.16.0 xtable_1.5-6
>>>>
>>>> Best,
>>>> David
>>>>
>>>> 2012/3/4 Wolfgang Huber<whuber at embl.de>:
>>>>> Dear David
>>>>>
>>>>> thanks. What's the output of 'sessionInfo()', and have you tried with an
>>>>> up-to-date version of arrayQualityMetrics?
>>>>>
>>>>> http://www.bioconductor.org/packages/devel/bioc/html/arrayQualityMetrics.html
>>>>> or at least
>>>>> http://www.bioconductor.org/packages/release/bioc/html/arrayQualityMetrics.html
>>>>>
>>>>> Let me know if the problem persists.
>>>>>
>>>>> Best wishes
>>>>> Wolfgang
>>>>>
>>>>> Mar/4/12 11:02 AM, David Westergaard scripsit::
>>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I am trying to use the BioC package arrayQualityMetrics to asses the
>>>>>> quality of a range of experiments. I am, however, running into errors,
>>>>>> when processing Affymetrix Hugene designs, particularly
>>>>>> http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-33443
>>>>>>
>>>>>> I'm using the following code:
>>>>>>
>>>>>> library('arrayQualityMetrics'); library('affy')
>>>>>> mixture.batch<- ReadAffy()
>>>>>> arrayQualityMetrics(expressionset=mixture.batch,
>>>>>>
>>>>>> outdir=paste("/home/projects/rgroups/cheminf/dwe/figures/self_processed/QA/",veggie[i],sep=""),
>>>>>> do.logtransform=TRUE,
>>>>>> force=TRUE
>>>>>> )
>>>>>>
>>>>>> And get the error:
>>>>>>
>>>>>> Error in setQCEnvironment(cdfn) :
>>>>>> Could not find array definition file ' hugene10stv1cdf.qcdef '.
>>>>>> Simpleaffy does not know the QC parameters for this array type.
>>>>>> See the package vignette for details about how to specify QC
>>>>>> parameters manually.
>>>>>>
>>>>>> Error in density.default(as.matrix(log2(mm(expressionset))), ...) :
>>>>>> 'x' contains missing values
>>>>>> In addition: Warning message:
>>>>>> In aqm.qcstats(expressionset) :
>>>>>> 'plot(qcStats)' from the package 'simpleaffy' failed for this dataset.
>>>>>> Error in obj[[i]]$legend : $ operator is invalid for atomic vectors
>>>>>> In addition: Warning message:
>>>>>> In arrayQualityMetrics(expressionset = mixture.batch, outdir =
>>>>>> paste("/home/projects/rgroups/cheminf/dwe/figures/self_processed/QA/",
>>>>>> :
>>>>>> Cannot draw the Perfect Match versus MisMatch plot
>>>>>>
>>>>>>
>>>>>> Now, from what I've read in an older mail to this list, Hugene is a
>>>>>> PM-only type design, building my own .qcdef wouldn't really do no
>>>>>> good. Googling around didn't really give any useful information. So
>>>>>> how do I get by this problem?
>>>>>>
>>>>>> Also, why do only some array types output a complete index.html,
>>>>>> providing the numbers for outlier detection?
>>>>>>
>>>>>> Best Regards,
>>>>>> David Westergaard
>>>>>>
>>>>>> _______________________________________________
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>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Best wishes
>>>>> Wolfgang
>>>>>
>>>>> Wolfgang Huber
>>>>> EMBL
>>>>> http://www.embl.de/research/units/genome_biology/huber
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org
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>>>>
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>
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--
Best wishes
Wolfgang
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber
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